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The protein structure prediction example (AlphaFold) is interesting, because the problem they’re addressing is not that we have no theory per se, but solving th
by rsfern 5y ago
The protein structure prediction example (AlphaFold) is interesting, because the problem they’re addressing is not that we have no theory per se, but solving the geometry optimization problem directly with ab initio quantum mechanical calculations is not computationally tractable.
- dekhn 5y agoProtein structure prediction is not a matter of finding the best geometry (lowest energy). That's simply not true with the except of the simplest two state folders that form trivial geometry.
- rsfern 5y agoSure, but you can search for local optima, and then there’s all the environment specific factors, solvation, finite temperature, that sort of thing. Really you want the local energy landscape so you can understand dynamics and stability. (It’s not really my field) My main point is, AlphaFold isn’t displacing any general theory that predicts structure from sequence. It’s displacing other machine learning systems, which are mostly displacing just getting/making the protein and doing the X-ray crystallography (where you really do have a straightforward geometry optimization problem) Again not my field so maybe I think about it a bit weird